[gmx-users] Block calculation

Justin Lemkul jalemkul at vt.edu
Fri Dec 23 19:21:41 CET 2016

On 12/22/16 4:26 PM, Kelsy Yuan wrote:
> Hi,
> I am working on a system that contains a mica block and some stearic acid
> molecules. The mica block is considered as a frozen group, and we are only
> interested in calculating the dynamics of the stearic acid molecules on top
> of it. When I try to minimize the energy of the system by using grompp,
> many errors occurred according to the force field of mica. Since all I need
> is an ionic surface for stearic acids and I do not interested in the
> dynamics of mica, I wonder is it possible to skip the force field part of
> mica? According to the Gromacs Manual, the frozen group keep stationary in
> dynamics, so I wonder can gromacs do calculation without checking the force
> field of the frozen group?

Freezing is a very artificial perturbation on the system, and you have to be 
careful to use proper energygrp_exclusions to avoid spurious contributions to 
the virial.  Faking your way through a force field model is something that 
should rightly raise eyebrows with reviewers.  Can you rightly call something 
mica if the force field is incompletely defined?  You might be better off just 
defining a set of charged dummy atoms if all you care about is a generic, 
charged surface.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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